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// $Id: likelihoodComputation2Codon.h 4699 2008-08-14 14:19:46Z privmane $
#ifndef ___LIKELIHOOD_COMPUTATION_2_CODON
#define ___LIKELIHOOD_COMPUTATION_2_CODON
#include "definitions.h"
#include "computePijComponent.h"
#include "sequenceContainer.h"
#include "suffStatComponent.h"
namespace likelihoodComputation2Codon {
MDOUBLE getTreeLikelihoodAllPosAlphTheSame(const tree& et,
const sequenceContainer& sc,
const vector<stochasticProcess>& spVec,
const distribution * distr);
MDOUBLE getProbOfPosUpIsFilledSelectionGam(const int pos,const tree& et, //used for gamma model
const sequenceContainer& sc,
const stochasticProcess& sp,
const suffStatGlobalGamPos& cup,
const distribution * distr);
MDOUBLE getTreeLikelihoodFromUp2(const tree& et,
const sequenceContainer& sc,
const stochasticProcess& sp,
const suffStatGlobalGam& cup,
Vdouble& posLike, // fill this vector with each position likelihood but without the weights.
const distribution * distr,
const Vdouble * weights=0);
};
#endif
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